A Brothers Worse Nightmare
by Criminalminds01453
Summary: Raphael is taken as a young turtle and for a year is tested on by the scientists that took him. His brothers find him, but this isn't the same Raphael that left. Hes angry at someone, They killed someone close to him. There will be four OCS.
1. Chapter 1

**Sup I'm min. So this is my first story for the turtles ever! I love the turtles especially Raph! anyway so basically Raph is kidnapped as a little turtle and a year later they find him scared and traumatized from what he saw. There will be 4 new OCs. Enjoy!**

**disclaimer: I don't own TMNT**

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><p>One day four little turtles were playing. They were no normal turtles. The oldest was Leonardo who loved the color blue and totally was a leader by birth. Next was Donatello, who loved the color purple and was the second oldest. The third oldest and a total goofball was Michalangol, who loved the color orange. The youngest was Raphael, he was queit and loved the color red. He followed his older brothers around everywhere. Their Father Splinter sent them to practice(play) in the sewers. Soon the sound of laughter filled the sewers. All the sudden the 3 older kids could not find their youngest brother.<p>

"Where's Waph?" Asked Leo

"I don't know weo." Said Mikey

"Donny Mikey go lookin the otder pipes for Waph." Instructed Leo

"OK!" Shouted mikey and Donny.

"Waph! Waph, come out please." Shouted leo. Soon screams sounded down the sewers. Leo ran in the direction of the scream as dogs barked. He turned the corner in time to see his youngest brother being loaded into a cage.

"Weo!" Shouted Raph as he saw his brother.

"Waph!" Leo shouted back. He reached up tto grab his hand but was too short. Raph was already top side. Leo knew if their father knew he would be in trouble but he needed to help his brother. He jumped up and was topside in a matter of minutes. He raced after his brothers startled cries. He sounded to be in alot of pain.

"WEO! WEO!" Raph shouted on top of his lungs.

"WAPH! WAPH I'M COMING!" Shouted Leo as he raced to his brother. He wasn't fatst enough and the van got away. Leo stopped running and started crying. he ran back to the manhole and jumped in.

"Donnie, Mikey, Waph got away." said Leo in a sad voice.

"Who gunna tell, daddy?" asked Mikey

"I don't know." said Leo "Hey Donnie, you tell fadder he will beweve you before he would me."

"Otay, Weo." said Donnie as they walked back. "Fadder, I have something to tell you."

"What is it, Doonatello?" asked Splinter

"We were twain' and these people got waph. Weo tried to get him, but the van was too fast for him." said Donnie, in fear of getting in trouble.

"Leonardo!" roared Splinter.

"yes Fadder?" asked a very terrifed Leo

"What happened?" asked Splinter

"Well, we were twain' then I noticed Waph was not near us, so we went to wook for im and den I heard a scweam and When I got dere Waph was in a cage and he was sweaming for me, but I couldn't weach im. I welly twied. I even followed dem to the surface." said Leo

"Could Waph not excape?" asked Splinter.

"No." said Leo "The bars were weally tick."

"We will find him." said Splinter.

"Otay, Fadder." said Leo

"Go train my son." said Splinter. The boys walked into the Dojo with the intent to get better, so they never have to lose another brother again.

"Hold on Waph, were coming." said The boys.

**Raphs POV**

When was leo and father gonna get here, I'm scared. These people are really scary. They look like the people father warned us about.

"Whats this?" asked a man

"A mutant, like the girls." said A another voice, this one sounded different, like the girls I see from the drains.

"Hi little guy." said the man again.

"I wanna go home." I cried

"You will after we do some tests." said The girl

"I wanna go home now!" I scream

"Later little one, whats your name?" asked the man

"Waphael." I say

"Well raphael, were gonna take you to your first test ok?" asked the female

"Otay." I say

"How old are you?" she asked

"5" I say

"Cool." she said and so began the first test. inside the first room, was a bed.

"lay on it." she instructed. I did. "Good, now this may hurt." she said as she turned on this machine. She was right, It hurt so bad, I screamed for Mikey , Donnie, Father, heck even Leo. I just wanted to go home.

"Its over little one." said The girl. I tried to fight her but she was so much bigger and it hurt to move. She took me back to the room with a bunch of cages in mine was another little form. The mean women shoved me roughly into the cage. The little form whimpered. She had long blaond hair and red eyes. She shook as I put my hand on her shoulder. I could feel feathers under her shirt. Sure enough when she came too, I saw big white wings. She looked to be my age.

"Hi." i say softly

"Hi" She said "I'm Lilly. What you name?"

"Waphael." I said

"Pwetty name." she said "I have 3 odder sisters, Wachael, Dani, and Mikey."

"I got 3 bwdders." I said "Leo, Mikey, And Donnie."

"Cool, It like our siblings are near enough in name to become fwiends." she said

"Yeah, Hey want to be fwiends?" I ask hesitantly.

"Yeah, We can pwotect each odder." She says

"Yeah. We could." I said. "How old are you?"

"I'm 5. You?" she asked

"I'm 5 too." I said in surpise. We talked for a long time. We talked about everything. Our families, How the dark coats got us. She really wanted to see her sisters again. She had been there since she was a baby. Soon enough we fell alsep near one another. My arm went around her as the room got colder. I remember Leo doing this when it was colder by the minute.

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><p><strong>So theres the first chapter. Hope you enjoyed this. Please R&amp;R. Like no one is.<strong>


	2. Chapter 2

**Sup? So,Thank you to all that have reviewed and favorited me or my stories. Please continue being awesome.**

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><p><strong>Raph's POV<strong>

So it has been a year since that fatal day. Since then me and Lilly have become each others saviors. We talk about everything. The scientists have experimented with our DNA. It really hurts. But the good thing is that now I can actually make my blood boil. I miss Leo and Mikey and Donnie. I just want to know they are OK.

"Willy?" I call as I crawl over to her. I forgot to mention that for some reason I still talk like a little kid.

"Yeah Waph?" Lilly asked

"Where's Wachael?" I asked

"Don't know , Why?" She asked

"Lilly? Raphael? Come here!" Rachael said. We were so busy talking we didn't notice Our cages were open. We ran out of our cages. Someone tried to grab me but I made my blood boil. The person dropped me in surprise as her hands started to burn. Yeah a side effect is that my skin burns up. It gets really hot but it doesn't hurt me at all. I dropped and executed a perfect flip. Leo would have been so proud. Rachael made sure we all knew how to defend ourselves. She trained us in the way of the ninja. The same way father was training us. I ran to the door, and when I reached the door, I ran for it. I grabbed Lilly's hand and we both booked it to the exit.

We ran through the center and we went to the forest. Rachael and the others soon caught up to us. I ran to them and grabbed their hands. They picked me and Lilly up and we ran through the forest. We were in a place called Los Angles. I is a big city, almost as big as New York. They snuck into an abandon car lot and hot wired a car. I know how they did it but I won't tell you because I don't want anyone to try it. I don't want people to get arrested for car theft. Soon we are on our way home. TO NEW YORK!

**Leos POV**

It had been a year since Raphael's disappearance. Everyone was on edge. Then spoken questions. What if they came back? What if we never find him? What if...? all the what ifs were still circling our minds. We were now faster, stronger, and smarter. We had our weapons. Raphs were still folded up in his blanket. It hurt me to remember when I lost him. It has been a year exactly. Soon there was some screaming coming form the pipes.

"Donnie, Mikey. Lets go someones in trouble." I shouted. I threw on my mask and raced down the pipes on my skateboard. The first thing I noticed was the two smallest of the 5 were holding their own as they fought 3 guys. then one of them went down and I heard a shreik of pure rage. The girl raced over to the other form and then even from 20 yards away, I could feel the heat from her radiating off her. I signal to Donnie and Mikey to get the unconscious form. Mikey and Donnie grabbed the form who I could now tell was a small turtle form. we grabbed him and started to run back to our pipe when we heard cries of the young ones name.

"Raphael!" called on voice

"Raphael!" called another

"Raph!" called another.

"Waph!" called a young voice. the boy in Mikey and Donnie arms stirred and all the sudden they dropped him.

"Wachael!" called the young one. Soon the 4 girls that had fought ran over to him and grabbed him.

"Your ok." said the one who looked like the oldest."Who are you?"

"I'm Leo and This is Donnie, and Mikey. You are?" I ask

"I'm Rachael and this is Dani, and Our Mikey. This little ones name is Lilly. The one on the grounds name is Raphael." said Rachael

"Weo." called the one they call Raph.

"Hi little man." I say as I realized that It is indeed my little brother. Mikey and Donnie came over and hugged us. We were a family again.

"Is this your family Raph?" asked Dani. Raphael shook his head yes. "Well then bye." She said

"NO!" he screamed as he grabbed the youngest and took her over to us.

"Raph. She has to go with them." said Donnie

"NO!" he shouted louder soon we could see smoke rise up from her hand. Her hand was in flames.

"Whoa!" Mikey said in surprise.

"Lilly, Raphael. Stop this, this minute!" shouted Rachael

"No, Stay pwease?" he asked

"Is it ok with your family?" she asked

"It will be. We will make father understand." I said. I hated seeing Raphael this disraught. I just wanted to make the look go away. Soon both Lilly and Raph were sound asleep. Rachael had both of them. We tried to separate them and we both got burned. I look at my hands and see they are blistered.

"So whats your story?" I ask as we walk through the tunnels.

"We were taken as little kids. They mixed our DNA with the DNA of a bird. We got stuck with wings. Lilly is the youngest cause she was named last. Both Lilly and Raph were tested on the most. They were in same cage. They can't sleep unless they are near one another. The one time we tried it we burnt down half the forest. They experimented on Raph with who knows what. all we know is one time he came back and he was able to literally make his blood boil." said Rachael "Well that's pretty much our story whats yours?"

"Well 6 years ago our father and us were knocked into a pile of ooze. And we started to mutate. Thats pretty much it." I say

"Cool." she says

"Do you have a mother?" I ask

"She died." is all she said.

"What about a father?" I ask

"None. He was never in the picture." said Rachael. We came to our door.

"Heres were we live." I said as I open the door. "Father? we are home!"


	3. Chapter 3

**Hi! So I'm Min and this goes for every chapter, I don't own The Turtles. I wish I did, but I don't. Anyway so this is when the girl's meet Splinter. Enjoy and as always, R&R! Oh, and both Makayla and Michelangelo will be called Mikey. Well Mike for male Mikey and just Mikey for the female Mikey. And Dani is Daniella. **

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><p><strong>Normal POV<strong>

The girls and boys walked in. Lilly and Raphael hid behind Rachael. She was holding onto them with a white knuckle grip. Mikeys' teeth were clenched. Dani was looking around like she thought the walls or shadows would jump out and grab her. Rachael was just looking around and she was obviously very scared.

"It will be ok." said Leo

"I know. I'm just jumpy." said Rachael

"Come here, Raph." said Donnie

"Otay." said Raph as he headed over to Donnie. As soon as he reached him, he clinged to him. Donnie just grabbed his hand and walked him over to the door of the Dojo.

"Father?" asked Donnie as he entered the Dojo. "We found Raph and others."

"What do you mean others?" said Splinter

"We found him with 4 girls." said Leo as he also walked in.

"Well bring them in if they are here." said Splinter

"Come in girls." said Mike

"I'm Rachael, This is Mackayla, Daniella and this is Lilly." Rachael as she pointed each one out. Splinter got up and walked over to them. Lilly hid behind Rachael even more.

"Hello little one." said Splinter

"Hi." said Lilly

"Are they trained in the way of ninjitsu?" asked Splinter

"We know how to fight." said Dani.

"Well I shall test..." said Splinter before he was interrupted.

"NO! NO TESTS!" shouted Lilly and Raph as they ran and hid in the corner. "NO TESTS! PLEASE!"

"He meant quiz. Lil', Raph, He meant quiz." said Rachael as she looked to Splinter.

"Yes. I meant quiz." said Splinter.

"Oh, OK." said Lilly and Raph as they calmed down but still had some tears running down their faces.

"Alright. Who shall go first?" asked Splinter

"Wach against Weo!" shouted Lilly

"Yeah!" shouted Raph.

"Ok, Leonardo, Rachael, please start to spar." said Splinter

"I'll take it easy on you." said Leo

"Oh, how considerate. But be ready to go down." Rachael said before she really let loose. Leo was stunned and was knocked down before he had time to think. He bounded back and started to really fight her. She still was kicking his butt. Then he pulled out his katanas. She saw this and jumped over him and grabbed the spare set. She spun them like she knew what she was doing. Again he was on the ground, but this time he had two katanas at his throat.

"What were you saying?" asked Rachael

"Nothing." said Leo "Would you be kind and remove the blades from my throat?"

"Oh, Sure." said Rachael as she backed up and offered Leo her hand. He took her hand.

"Whos Next?" she asked

"Donnie vs. Dani!" shouted everyone but the mentioned parties.

"Your are going down. You will bow down to my supreme intelligence." said Dani "Also I heard you have a lab, can I see it after?"

"Sure." said Donnie as they started to fight.

"Wachael?" asked Raph as the two fought.

"Yes?" said Rachael

"Can we mediate?" asked Lilly

"Sure." said Rachael as they got down on their knees. The two started to meditate as the fight wound down.

"Okay, So Mikey V.S. Mikey?" asked Leo

"Yeah!" said Everyone.

"Fight!" yelled Rachael

"Shh!" yelled Raph

"Sorry, guys." said Dani

"What are they doing?" asked Donnie

"Meditating." said Rachael

"You guys meditate too?" asked Leo as he kneeled down in front of Splinter.

"Yes also Lilly and Raph both use sais." said Dani. "I use a bow staff and Mikey uses nun-chucks."

"Wow." said Mike from his place on the floor. Mikey was on top of him with a knife pulled.

"Mackayla!" Rachael yelled startling everyone.

"Ok how about Lilly against Raph?" asked Donnie

"NO!" yelled Mikey, Dani and Rachael in unison.

"Why not?" asked Splinter

"We'll be here for hours waiting for them to stop." said Mikey

"Whats the record?" asked Dani

"5 hours." said Rachael

"Oh yeah." said Dani.

"OK, How about Leo and Mike against Lilly and Raph?" asked Donnie

"Ok." said Lilly and Raph in unison.

"Alright, GO!" said Rachael as she stepped back. Lilly and Raph stepped forward and attacked. In a matter of minutes, the weapons were drawn. Soon both Leo and Mike were on the floor. Lilly and Raph were barely breathing hard, while Leo and Mike were breathing heavily.

"Wachael? I'm hungry. Can we have cookies?" asked Lilly as she and Raph came over.

"Sure. Oh, and go color." said Rachael

"Only four, you two. Only two cookies." said Dani

"Why only four?" asked Splinter

"Because they will go haywire from all the sugar." said Mikey

"Oh, so they're like Mike after three bowls of ice-cream?" asked Leo

"Does he destroy an entire building on a sugar high?" asked Rachael. They walked into the living room to see Lilly and Raphael drawing contently on the floor.

"When's lunch?" asked Raph.

"In a little while." said Splinter as he headed for the kitchen.

"would you like us to cook?" asked Lilly

"Why yes. If it is alright with your sisters, that is." said Splinter

"You two can." said Rachael

"Come on Raph." said Lilly

"OK, Lilly." said Raph as they headed to the kitchen. Soon there was a crash in the kitchen.

"Lilly!" yelled Raph.

"Oh boy." said Rachael

"This is going to be, a weird experience." said Leo

"definitely." said the others in unison. They all started to laugh at the same time, from them talking at the same time.

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><p><strong>So basically Raph and Lilly will talk their age as the become more comfortable with everyone. Don't worry the next chapter is when the death will happen. So anyway, R&amp;R!<strong>


	4. Chapter 4

**In the turtles home  
><strong>

As the children entered the kitchen, the first thing they noticed was how easily, Lilly and Raph handled a knife. And how quick they both were with said knives. They both were using chef knives that they had scavenged from a junk yard. Splinter came into the kitchen as Lilly and Raph put a pot of water onto the make shift stove. Then Lilly and Raph added celery, carrots and onions which were also found in a yard. Soon the house smelled of the delicious food being prepared.

"What are you guys making?" asked Rachael

"We are making tomato soup with crackers, and also we are making tomato sauce for dinner." said Raph.

"It almost done?" asked Leo

"Be done in about half an hour." said Lilly

"Be back in thirty minutes." said Mikey

"Alright." said Raph

"You need help setting up the table?" asked Donnie

"No we'll do that as the soup is cooking." said Lilly

"Alright, be back soon." said Mike

"Bye, bye." said Raph as he and Lilly went to set up the table. Soon enough dinner was ready. The guys followed the girls in cautiously. They didn't know what to expect from little kids, even if one was their little bother. Both children put up bowls of soup that were still steaming. Soon the bowls were set and everyone started to eat. At the first bite of the delicious soup, they couldn't eat it fast enough. Within five minutes they wanted more. the two children were more than happy to obliged, glad the boys loved the taste of the soup.

"Rachael, I'm tired can I go take a nap?" asked Lilly

"Sure. Raph are you tired?" asked Rach

"A little bit." said Raph

"OK, Well why don't you go sleep in the living room. We'll call you when the sauce is almost ready." said Dani

"OK." said Lilly and Raph

"Night." said Leo. The others went back to the dojo to practice more. Everything was quiet till terrified yells filled the lair.

"Whats that?" hollered Leo over the noise

"Lilly and Raph." said Mikey

"Crap." said Rachael as she ran into the room. Lilly and Raph were clinging to each other and their screams quieted down to loud sobs. Rachael saw the floor underneath them glowing red. smoke rose from Lilly and Raph. Dani raced over and grabbed both Lilly and Raph and Ran them into the kitchen.

"Raph! Raph! Buddy wake up." shouted Leo

"Lilly! Lilly! Come on sweet pea, wake up." shouted Mikey

"No! Raph! Sissy they're hurting me! Make them stop!" Lilly screamed.

"Leo! Leo, help me!" Shouted Raph as he flaied around. After ten minutes of this, both Lilly and Raph woke up and ran to either Rachael or Leo. Lilly had bloody tears running down her face. Raph had pure blood. The others were shocked to see this. Raphael just sobbed into Leos shell. The tears still running down his face. Leo sat there rubbing his shell in comfort trying to get him to calm down enough so he wouldn't cry so much he would get sick. Raphs shell seemed to radiate heat.

Lilly was still sobbing and she cried because she was not near Raph. Leo and Rachael put both little ones next to each other.

"Lilly,what happened this time sweetie?" asked Rachael

"They, they killed you, an-and Dani, and Mikey and our new friends. I was just me and Raph and then they shot him. It was like they never wanted to go away. Why are they after me in my dreams too? It was the one place I could escape to. Why?" Lilly shouted

"Raph?" asked Leo

"Same but it was you guys." Raph practically sobbed.

"Shh, Shh its OK, your OK." said Leo

"You won't let them take me right?" asked Raph as scared as he was.

"I will never let you go." said Leo

"We never would." said Donnie and Mike

"OK. Can we go into the sewers to train?" asked Lilly

"Sure, Meet you boys out there." said Rachael.

"I'll come with you." said Raph

"NO. You can not." said Dani

"I hate you." yelled Raph. Those were the last words he ever said to his sister. A little while later, he and his brothers were racing through the sewers looking for their new friends. Raph went one way, Mike went another, and Donnie and Leo went another. a scream split the air. They all raced to where it came from. They turned the corner and the sight in front of them made them stop. Raph was kneeling in front of a body. Judging by the size they judged it to be Lilly.

Raph was sobbing into his hands. Leo went to him and tried to put his hand on his brothers shell. Raph pushed away his brother. Raphs skin was red hot. It hurt Leo to be near him. But he forced himself to be. He would be there for him even he didn't him want to be. Raph suddenly got up and ran down the pipe. He ran back to the lair. He threw open the door to his room and slammed the door. No matter how hard his brothers begged, and pleaded, he would not come out of his room. Eventually he let Leo into the room. Leo stayed in the room all night.

**Rachaels' POV**

We raced down the pipe. We saw Mother and we all hugged her.

"Children your OK." said Mother

"We're fine Mother." said Lilly

"We have got to go." said Mother

"What do you mean?" I ask

"The boys told the scientist where were are." said Mother

"Raph and his brothers would never do that." shouted Dani

"No time for arguments!" said Mother "We need to go now."

"They would look for us." said Mikey

"I have a way to buy us time." said Mother

"OK." said Lilly sadly. We looked back to the one place we had felt safe and then we left. We had only been there not even a full day but it would always be home.

"Guys." I say "If anything happens come straight here. We'll meet up here." I say

"OK." said all the others.

"Bye, Leo." I whisper before turning and walking out into the bright sunlight.


	5. Chapter 5

**8** **1/2 years later. Raphs' POV.  
><strong>

It has been over 8.5 years since Lilly was found dead. Since she and her sisters were murdered. It was our 15 birthday. I couldn't believe it had that long. As I head into the kitchen I see my brothers looking at me.

"What'cha ya lookin' at?" I ask

"Nothing." Donnie says quickly.

"Come on. Its time to go top side." said Leo

"Lets go." I growl before the tears pricked my eyes. Over the last few years whenever we could go topside I would. Hoping what my eyes saw was not real. I was always the first one topside and the last to return from patrol. Before, on the day she died, I would lock myself in my room and just hide. At night the tears would fade as I slept. Other night I would have nightmares so bad, I would have to run to Leo. Only he knew I cried for her. The others suspected but don't know the truth. Each year was different. I would either stay in my room and cry or go topside and patrol till I collapsed from exhaustion.

The years I would stay in my room, I would wear sunglasses to block out my eyes so Donnie and Mikey wouldn't see the red around them. I have been more violent since her death. I fight with them all the time. I couldn't help it. Lilly had burned to death. She had been burned by those scientist. Even Donnie is scared, that with my hatred of scientists, that I would hate him. That I would hate him for his passion for the sciences. I don't. I am I thrilled that he is going to be a scientist, No. Do I hate him, No.

As soon as I was topside, I went up to the roofs above Aprils. April reminds me of Lilly, same temper and fiery nature. Same color hair too. I used to wonder when we first met her if she was Lilly under a different name. Now I know she isn't like Lilly. Lilly would be right here with me, fighting. She wouldn't be telling me to be careful, to be safe. No, she would be the one keeping me safe. She would be telling me every time I got hurt, how stupid I was and how badly I scared her. God, do I miss Lilly.

"Raph!" called Leo

"What?" I say irritated

"We got company." was all he had time to say. Four figures dropped onto the roof and immediately attacked us. This was a new area. We had never patrolled here before. Casey had, but a few nights ago he got hurt pretty badly. These guys were tough. The one I was fighting was seemed familiar, but I couldn't put my finger on it.

"Shell!" yelled Donnie as he was struck in his stomach. I immediately dealt with the girl I was fighting an ran to Donnie.

"Ya alright?" I ask

"fine." said Donnie

"Stop!" Yelled the one who looked like the youngest.

"Why?" asked the oldest.

"I think we're fightin' the turtles." said the girl

"Wait, Mikey" asked one of the others

"Mackayla?" asked Mikey

"OH MY GOD!" the girl shouted

"No way." said Mikey

"Raph?" asked the one I had been fighting

"Lilly?" I ask hoping this wasn't one of those dreams.

"Oh my god, it is you!" she shouted

"Oh my Shell." whispered Donnie.

"You said it. Hey, Donnie." said Dani

"Hey, Dani." said Donnie

"Hello, Leo." said Rach

"Hey." said Leo before hugging her like he was never letting her go.

"What are you guys doing here, and alive at that?" asked Mike

"What are you talking about?" asked Rach as she pulled away from Leo

"I found your burned bodies." I said

"Wait, This was mothers plan?" shouted Rach

"What do you mean." said Mike

"Mother said that you guys would sell us out to the scientists. We had to leave with her. She said she had a way to make sure you never followed us." said Mikey

"What a b*****." said Leo

"You said it." said Lilly as familiar music played.

"Shall we dance?" I ask remembering the time in Vegas when we danced to this very song.

"We shall." said Lilly as she pulled me close. Rachael grabbed Leos hand and had him dance with her. Mike and Mikey danced as did Donnie and Dani. We just danced and danced as the night slowly turned to day. We were all tired and we just wanted to go home, but Mike wanted to check on Casey, and April. So we headed to Aprils'. The girls seemed jealous at first but they had no reason to. I mean we weren't even going out with them. _"Y__et." _my mind whispered. I don't know when the feelings I had for Lilly went from brotherly to more than just friends, and I don't think Lilly did either.

"Who's this?" asked April quietly as she let us in through her window.

"This is Lilly and her sisters Rachael, Daniella, and Mackayla." I said as I helped Lilly through. As soon as we were all set, she fell asleep. I soon joined her in dreamland. I believe the others did too, seeing as a little while later as we all woke up and the sun was setting. The others were still out. Hearing voices in the kitchen, I headed into the kitchen.

"Raph, I heard you and Lilly used to cook, is that true?" Asked April.

"Yeah we did." I said as I took a seat next to Lilly. I was still amazed at the fact that she was here, and she was safe.

"Me and the others were just passing through but we heard reports about you guys so we decided to stick around. We at least, I had hoped you were still here." said Lilly

"I have hoped that that day, the day you 'died', you were still alive. That it had all been a mean prank. But as the days wore on to weeks and then weeks to months and so on, that you were really dead. I didn't want to believe that. I, no one knows this but Leo, I would cry everyday, thinking I failed you. We promised each other, we would never leave one another. That we would always protect each other and I failed. I broke that promise. I still feel like that." I admit as the tears fell down my face "I still feel like that."

"Oh, Raph. I always felt that _I_ failed _you_. Not saying goodbye. Not trusting you. Our mother had said that but I believed her. I know it was all her plan to get us back, but I should have tried to get here before know." said Lilly

"That's silly, Lilly. I guess we both goofed up huh?" I ask

"Hey, Raph?" April asks

"What?" I said

"You lost the Brooklyn accent." said April

"Oh, yeah, I guess I did. Actually the only reason I sounded like that was to put others off, to not let them see how much pain I was really in. I mean besides Leo and Casey." I say

"Well, I like you better without the accent." April says

"Me too," said Donnie

"How long have you been there?" I ask

"Since you started talking to Lilly, about how you felt you failed her." said Mike

"I would kill both of you, BUT Lilly is here and you guys have to remember, I was less violent with her around." I say

"I remember." said Mike

"You also have less of a temper, because if she wasn't here you would have beaten us by now." said Donnie.

"That too." I said as we all laughed. I forgot how good t felt to laugh. How carefree. How light I had felt all those years ago.


	6. Chapter 6

**Hey, so I just finished A dark side, so I have more time to update this. I have no clue where to go with this, I'm think of going TMNT, the '07 version.**

**Disclaimer: I only own my OFCS.**

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><p><strong>After Leo Leaves.<strong>

Its been a while since Leo left. I remember the day like it was yesterday.

_As I walk into the house, I hear Sensai call Leo and Rachael into the Dojo. After a while I fall asleep, holding Lily in my arms. We are both so tired. I can barely move. The next morning, I wake up and Leos gone. So isn't Rachael. Lillys crying in the corner with both Mikey's trying to console her. _

_"Whats wrong?" I ask_

_"Leo and Rachael Left for training in south America." said Mike  
><em>

_"What?" I ask in disbelief._

_"They left." said Lilly as tears ran down her cheeks. I go to her and collapse next to her. Tears came to my eyes. _

_"Donnie and Dani, are in charge." said Splinter  
><em>

_"But father, Why?" I ask quietly_

_"They went away to become better leaders." father says _

_"Why? Why did they have to leave?" asked Lilly_

_"Its easier if they aren't distracted." said Father_

_"You mean by us." said Mike_

_"No by things in general." said Father. He want continue but I left. How could Leo do this? I mean he knew how much I need him._

So its been a little over a year. They both stopped writing a little over a six months ago. Today me and Lilly were moving out. For awhile I was a the Night Watcher, but then Lilly made me see reason. I couldn't hurt people even if they were criminals. We couldn't stay at the lair anymore. We already told Father. I just couldn't do it. It really hurt me to think he forgot about me but the thought has been popping up more, and more.

"father, we are leaving." I say as I enter the dojo, probably for the last time.

"Ohh, why are you leaving at night?" asked Father

"It would be better for them if we left at night, less stress for the others." I say, even though I want to say it is because Leo and Rachael left at night. "Please don't tell the others. Heres our number, let us know if they come home."

"I will my, son." said Father

"Ready, Raph?" asked Lilly

"Yeah. Bye Father." I say

"Bye, my son." said Father

"Tell the others goodbye." said Lilly as we pick up our bags and leave. I look around one last time. I know its going to be awhile before I come back. The memories come back. I see us boys playing around. In the dojo to fight. I see father scolding me for fighting with Leo. I smile as the tears fill my eyes.

"You, OK?" Lilly asks

"Yeah, just thinking over some memories." I say

"Me, too." she says as she takes my hand. I turn to face and kiss her. With that we turn and leave the lair. We exit the sewers closest to our new apartment. I personally like it. I feel its like home. The dark walls and the natural stone counter top reminded me of our old home. Well the way home was before Leo and Rach left. I mean how could they. And to stop writing? Thats bad enough, not to mention it tore Mike, and Mikey to pieces. It tore at me and Lilly even worse.

It was awhile before me and Lilly unpacked everything. I had no Idea we had this much stuff. Seriously, it was like a zoo or something. Lilly put all of our weapons into the closet in our room. A few hours after we left, we finally finished unpacking. All we had left to unpack was Lillys clothes. We would leave that for later. I couldn't believe we really left. I mean I'm glad an all but it feels strange to be somewhere my family isn't.

"Hey Raph?" asked Lilly

"Yeah?" I say

"Do you think we'll be able to live without them?" asked Lilly

"I don't know. For a few days it will be odd, I'm sure. But soon enough it will be second nature. And when we go visit it will seem to loud." I say

"I hope so. My whole life, I was with my sisters and I never was really alone. Now that we are on our own, I can't help but wonder what will happen." said Lilly

"Me too Lil', Me too." I say before we both drift off to sleep. The next morning, me and Lilly decide to check out the neighborhood. I, for obvious reasons, wore my trench coat and hat. The neighborhood was beautiful. There was a park close by and a playground in the back of the apartment. We both feel as if they are never coming home. God, I miss them.

**Inside the lair.**

"Where are Lilly and Raph?" asks Dani as she and Donnie walk into the lair.

"Yeah, where are they?" asked Donnie.

"They moved out." said Splinter

"What are you talking about?" asked Dani

"They moved out. They do not wish to live here anymore." said Splinter

"Why?" asked Mike as he walked out of his room.

"They said they couldn't, I don't know if they'll visit, but I know that they still love you guys." said Splinter sadly as he walked out of the room.

"They left because Leo, and Rachael left. Think about it. They were really close to them and now they left. Just like them." said Dani

"God, your right." said Mikey

"I can't believe that they would actually leave though." said MIke

"I know, Mike, I know." said Donnie as mike broke down in his arms. All most all of his family left him.

"Are you guys gonna leave me too?" asked Mike in a scared voice.

"NO." said Donnie and Dani in unison.

"Never." said Mikey

"Good, I don't want to lose you guys too." said Mike. Little did the turtles know that Splinter was watching. HE took the number and called up Lilly and Raph.

_"Hello?" _said Lilly

"Hey, Its Splinter. You need to come over. Mike and Mikey think you abandoned them."

_"We'll be right over." _said Raph

"Don't tell them I told you. Call it an instinct or something." said Splinter.

_"OK, Be there in like 5." _said Raph

"Bye." said Splinter

_"Bye." _said Lilly as she hung up.

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><p><strong>Happy Holidays!<strong>


	7. Chapter 7

**Sorry! *dodges a pitchfork and other stuff.*I have been busy. OK I haven't been that busy but I lost inspiration for this story, then I started to read other story's. Blame my friends! I watched like ten minutes of HTTYD 2, And now I can't stop reading the fics for it. Then I like forgot to update, so again SORRY! Also, I'm going off of its been two years till they come home. So its been a year and a half already.  
><strong>

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><p><strong>Lillys POV<strong>

As we walked out, I saw that it was pitch black. Good, me and Raph don't have to worry about people seeing him. We walk over to the nearest manhole cover, and get in. On the walk to the lair, I wondered what we did to make them think we didn't love them.

"Lilly, You OK?" asked Raph

"Just thinking." I say

"Me too." says Raph

"Why would they think we hate them?" I ask

"I don't know." said Raph

"I miss them." I say

"Me too." said Raph "Even though it was only yesterday we saw them, I feel like it was days, weeks ago."

"I know Raph, I know." I say as I grab his hand.

"I miss Leo." says Raph.

"Me too." I say

"Do you think they hate us?" asked Raph

"I don't know." I say. As we walk into the lair, I see Mikey and Mike sitting on the floor.

"Sup?" I call

"Lilly! Raph!" called Mike and Mikey

"Hmm?" asked Dani as she exited the lab.

"Raph!" cried Donnie as he came out of the lab.

"Hey!" called Raph as he gave both of them a hug.

"Sup!" I yell as I hug Dani and Mikey.

"We thought you hated us." said the both of them.

"I'm sorry. Its just hard without Leo and Rachael here." said Raph

"We understand." said Dani

"Its hard for us too." said Donnie

"Well, we're here. How much quieter is it without us?" I ask

"Not much. How much quieter is it for you guys?" asked Dani

"Pretty quiet. Its actually hard to imagine it being that quiet here." said Raph

"Wow." said Donnie. We sat there for a few hours just talking. It was nice to talk to my siblings without a fight. Before I don't think we ever talked that long without a fight. I guess leaving makes one love the others faults more. I missed them but it almost a relief to leave. The noise was starting to get to me. I could tell it was bothering Raph too.

"You, OK?" I ask him

"I will be. I forgot how loud they were during the day and into early night." said Raph.

"Me too." I say.

o0O0o

**A few months later: Normal POV**

Lilly and Raph were walking in the park, all around them was young couples making out.

"Eww. Can they act anymore lovey-dovey?" asked Lilly

"What you don't like showing affection outside of the house?" asked Raph

"Its not that. I do, but can they not, like, almost have sex in public?" asked Lilly

"I guess not." said Raph as he pulled her close.

"Thank god for fog." said Lilly

"Why?" asked Raph

"Because then we can do this." said Lilly as she was spun.

"I like the fog to." said Raph

"Raph, I have something to tell you." said Lilly

"Oh no, Why does it sound like you are going to break up with me?" asked Raph

"Don't worry, I'm not." said Lilly

"OK, then what is it?" asked Raph

"I'm pregnant." said Lilly

"What?" said Raph in shock

"We're having a baby." said Lilly

"oh, my gosh." said Raph as he picked her up and swung her around. "How much longer till your due?"

"The doctor thinks I'm about four months." said Lilly

"Wow. Wait, what are gonna tell the others?" asked Raph

"What do you mean?"

"Umm, they need to know. What are we gonna tell them?" asked Raph

"Oh, I haven't actually thought about that." said Lilly

"Well they have a right to know." said raph

"What will your father say?"

"Forget that, what will our siblings say?"

"Oh, god that even scarier than telling your father."

"I know."

"What will we do?" asked Lilly

"Umm, I don't know." said Raph

"Your helpful." said Lilly

"Why don't we tell father first, then tell the siblings?" suggested Raph

"That will work." Said Lilly

"OK, lets head to the lair, and Tell father." said Raph

"Your ready." said Lilly

"I just want to get it over with so I can die in peace." said Raph

"What do you mean?"

"Well, If Leo and Rachael find out, I'm gonna be killed by Leo, then brought back and killed again by Rach, for getting you knocked-up. Plus If I don't die when we tell father, You know Donnie, and the others will be willing to kill me." said Raph

"True. Your dead." said Lilly as she coasted down through the sewer opening and landing. They walked or in Lillys case flew through the sewers, with Lilly cruising ahead sometimes, and sometimes drifting near Raph. She was super nervous. Raph on the other hand was relaxed. Normally it would be the other way around. but Raph was confident that they wouldn't kill him yet. Lilly flew up to pull on the lever to let them in. They make their way to the dojo, toward Raphs father.

"Father, may we talk to you?" asked Raph

"Yes, Raph? What is it?" asked Splinter

"I'm pregnant." said Lilly

"Excuse me?" said Splinter

"We're having a baby." said Raph

"OK." said Splinter

"What?" said Raph

"I wish that you would wait a few years, but I am OK with it." said Splinter "but you have to tell the others."

"Thats fine. We were going to tell them anyway." said Lilly

"OK." said Splinter

"Well, we'll go tell them." said Raph

"Go." said Splinter.

"Guys." called raph.

"Yes?" said Donnie

"We have something to tell you." said Lilly

"What?" asked Dani

"I'm pregnant." said Lilly

"We're having a baby." said Raph at the same time.

"Huh?" said Mike

"You'll be an Uncle." said Lilly slowly.

"OK, So how much longer before we deal with a baby Raph?" asked Donnie

"Um, About 5 or 6 months." said Lilly

"OK." said Dani as she raced for ward to hug Lilly. Apparently the news had just sunk in. Soon everyone was surrounding them, Hugging and congratulating them.

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><p><strong>So the next CH is about when Leo and Rachael will come home. Also R&amp;R.<strong>


	8. Chapter 8

**So now Leo and Rachael will come back. Also Lilly will disappear instead of Leo. Instead of asking the people who wrote this what will happen, JUST READ!**

**Disclaimer: I own nothing!**

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><p>As They walked back Lilly and Raph held hands. Thoughts flying through their minds.<p>

"Whats gonna happen if Leo and Rach come home before the baby is born?" asked Lilly

"I don't know. We probably would need to tell them." said Raph "Plus, Donnie and Dani would tell them before we could."

"I know, right? I mean thats our secret." said Lilly

"I miss them." said Raph

"Me too, Raph. Me too." said Lilly as they hop up the fire escape. The apartment was cool. Lilly shivered.

"You cold?" asked Raph

"A little." answered Lilly, "According to Donnie, My temperature will fluctuate."

"OK, I will keep that in mind." said Raph as he got her a blanket.

"Thank you." said Lilly as she snuggled into the blanket. Soon she was asleep on the coach. Raph picked her up and brought her into their bed.

"Night, Lilly." said Raph as he crawled.

"hmm." mumbled Lilly, as Raph chuckled. He was surprised she was awake. She was out as soon as he put the blanket on her. '_Wow, She is really tired. She normally is awake by now.' _As he pulled the covers over them, he was out before dawn broke over the horizon.

As time went on, Lilly and Raph made a lot of changes to their home. They were in the process of putting together the crib when the phone rang.

"Hello?" asked Lilly as she picked up the phone.

_"Its Splinter." _said Splinter

"What's up?" asked Lilly. She was worried, Splinter only called when something was wrong. Besides the day he called to have them go over, he hasn't called since. Lilly and Raph still visited the lair often.

_"I am calling to tell you that Leo, and Rachael are home." _said Splinter

"What?" asked Lilly in a shocked voice.

"Whats wrong?" asked Raph

"Leo, and Rach. They're home." said Lilly.

_"I was hoping that you would come down here and tell them the news." _said Splinter

"OK." said Lilly as she hanged up the phone.

"Are we going?" asked Raph

"Yes." said Lilly in a robotic tone.

"OK." said Raph.

o0O0o

Before Splinter called Lilly and Raphael, Leo and Rachael walked in.

"Father?" called a voice as they walked into the lair.

"Leo?" asked Splinter as he looked out of the dojo. It was indeed his eldest son, and eldest daughter home.

"Yes, Father, we have returned from training." said Leo as he knelt in front of his father.

"I missed you father." said Leo as he hugged his father.

"I missed you too, my son." said Splinter "Go tell your brothers your home."

"Yes Sensai." said Rachael

"Mikey! Dani! Donnie! Mike! We're home!" shouted Rachael "Raph! Lilly!"

"Raph, and Lilly aren't here." said Mikey as he rubbed sleep from his eyes.

"What do you mean, Their not here?" said Leo

"They moved out like 6 months ago." said Mike

"Why?" asked Rach.

"No idea." said Donnie

"I'm glad your home." said Dani

"Me too. Nothing beats New York." said Leo

"I know. They're still in New York, but we don't know where." said Donnie.

"Does Splinter?" asked Leo

"I don't know." said Donnie

"Father? DO you know where Raph, and Lilly are?" asked Rachael

"I do. But I was requested to not disclose such info." said Splinter

"Will they come to visit?" asked Leo

"I do not know, my son." said Splinter

"OK." said Rachael. They all settled down and talked about all that has happened in the last two years. Leo, and Rach, told, them about South America. Donnie and Dani, told them about the stuff the learned and about their jobs. Mike and Mikey told them about the times they had being entertainers. They ahd missed each other. Soon the lair door slid open and Lilly and Raph walked in.

"Hey." said Raph

"Hi." said Lilly

"What, no hug for your siblings?" asked Leo

"None." said Lilly betrayal coloring her voice.

"Whats that tone for?" asked Leo shocked

"No reason, I'm just angry." said Lilly

"Why? Because we left?" asked Leo

"Yes. And another fact, but I won't tell you." said Lilly

"What the other fact?" asked Rachael

"I'm not telling you." said Lilly

"Oh, come one. We tell each other everything." said Rach

"Leave her alone." said Raph in a dangerous tone.

"What the hell is going on with you two?" asked Leo

"Yeah, you guys seem pissed at us for some reason, but you won't tell us!" said Rachael as her voice slowly rose to a shout. Lilly put her hands over her ears and tears filled her eyes. She went into the corner and curled into a ball. Well as well as she could when she was six months pregnant.* Raph went to her to try to calm her.

"Lilly, Lilly. Its OK." said Raph as he tried to calm her. Soon she was screaming from the pain in her stomach.

"Donnie!" Yelled Raph

"What?" asked Donnie

"Somethings wrong with Lilly." said Raph as he picked Lilly up.

"Bring her in here." said Donnie "Leo, and Rach, Just wait out here."

"Why?" asked Leo

"Just do it." said Dani as she entered the room Lilly, Raph, and Donnie entered.

"Raph get me a hot compress." said Donnie

"Kay," said Raph in a whisper. It was the quietest they had ever heard him speak.

"You, OK?" asked Dani

"Not really." said Raph

"Tell me whats wrong?" asked Dani knowing it would help him to talk.

"I'm scared. I'm scared that something is really wrong and I won't be able to help her. I'm terrified that some how she'll lose the baby and maybe her life." said Raph as he started to cry. "I'm scared I'm going to lose they only good thing in my life, in a long time."

"I know how you feel. Lilly has always been the light, even in our deepest struggles. A few years ago, I wasn't sure I wanted to be here anymore, If I wanted to be a mutant, I was about to kill myself. She stopped me." said Dani as Donnie hooked Lilly up to a heart monitor.

"Might not need it, but I would rather be safe then sorry." said Donnie

"OK." said the other two.

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><p><strong>AN: Hey, So I don't know anything about being pregnant, so I am really winging it, on what I heard. Anyway R&amp;R!<br>**


	9. Chapter 9

**Sup! So as many know I am a huge fan of the TMNT Movie. Love it! Anyway, On with the show. Also this is he big fight scene. I changed it up a bit. And by a bit I mean a lot.  
><strong>

**Disclaimer: I own nothing but my OCs.**

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><p><strong>Normal POV<strong>

"Do you think shes OK?" asks Leo

"NO idea. Thats never happened before." said Rach

"What about them being moody and defiant?" asks Leo

"That happened when they were angry. Wasn't Raph like that before we were here?"

"Yeah, now that you mention it."

"Well, thats what happens when they want to either hide something, or their angry."

"Well, they're angry, so that must be it." says Leo as Donnie walks out.

"She OK?" asks Rach

"She fine, She'll be fine by tomorrow. She took a blow to the stomach a few months back, so now it bugs her when shes stressed." said Donnie being close to the truth as possible without giving away the to much.

"OK." said Leo not suspecting anything.

"Good, see you in the morning." said Donnie as he walked out.

"Cool." said Leo

**Inside the room.**

"You, OK?" asks Raph

"I'm sore." said Lilly

"I know, just try to relaxes." Raph said

"I'm trying." said Lilly

"I was so scared for you, and our baby." said Raph

"I was too," Said Lilly

"I'm so glad your OK."

"Me too,"

"Want to go home?"

"Yeah, I would like to."

"OK, I will see if Donnie is willing to let you go." said Raph

"Yes, hurry!" Lilly practically screamed.

"Kay," said Raph

"Donnie, Is Lilly able to go home?" asks Raph as he walks out the door.

"Yes, she is. I was waiting for her to wake up." said Donnie

"Kay, I will tell her." said Raph

"Lilly did you hear? You can leave." said Donnie

"Yes," said Lilly getting up and dancing around the room.

"Wow, shes really happy to leave." said Leo

"Yeah, She is." said Raph.

"Why?" askes Rach

"No idea." said Raph, as he lied to them.

"Kay," said Rachael as he walked in and walked out with Lilly holding her hand.

"Lets follow them." said Leo

"OK." said Rachael

"Where are you two going." asked Mikey

"Patrol." said Leo

"OK." said Mikey as they headed through the door.

Where are they?" askes Leo

"No idea." said Rachael

"Look, there they are." said Leo as he speeds off towards them.

"Leo!" yelled Rach at Leo as he raced towards them.

"Raph, what the hell is wrong as you?" yelled Leo

"What do you mean?" yelled Raph

"Since we got back, you have been lieing to us and hiding something. I am sick of the secrets and lies. Why won't you trust me?" asked Leo

"Why? Why should I trust you? ALL YOU HAVE DONE SINCE YOU GOT BACK, IS ORDER US AROUND! I AM SICK OF IT! JUST LEAVE US ALONE!" yelled Raph

"Rah, Whats going on?" asked Lilly as she walked up onto the roof.

"Nothing, Lilly go back downstairs." said Raph

"No, whats the big secret?" yelled Leo as he pushed Raph.

"Stop it! STOP IT, FOR GODS SAKES, LEO! JUST LEAVE US ALONE!" yelled Lilly

"Why?" yelled Leo as he turned towards Lilly. Lilly just turns around and flees over the roof tops. She doesn't stop even when she hears Raph calling to her.

"Lilly!" yelled Raph. Lilly just keeps running. She runs for a few more rooftops and then stops. She raced through the rooftops. A sound comes from behind her. She stops. She hears a high pitch whine and feels a prick in her arm. She does the only thing she could. She whips out her sais but no one is behind her. She collapse on the roof, with a scream.

"Raph!" yelled Lilly

"Lilly!" yelled Raph as he raced through the roof tops. "I'm coming!"

"Raph, Wait!" Yelled Leo and Each.

"LILLY!" Shouted Raph

"Raph," Lilly whispered as she was picked up and carried down the stairs. She was thrown into a truck, and the truck drove off. Raph gets to the spot he last saw the men he loved.

"LILLY!" Shouted Raph in pain. He looks all around and see her being put into the truck. He jumps down and and races after the truck as it starts to drive away. "LILLY!"

"Whats wrong, Raph?" asked Leo

"They took her. They F-ing took her!" shouted Raph

"Raph, come on we need to go. We'll go back to the lair and see if we can locate her." said Leo

"Fine." said Raph in a defiant tone.

"Raph, What is wrong, my son?" asked Splinter

"People, someone took Lilly. They took her." said Raph

"Who?" asked Donnie

"People, like stone people. I can't understand why they would take her." said Raph

"Thats crazy." said Donnie "Thats impossible."

"Well, we saw them too." said Leo

"OK, but that still not possible." Said Donnie

"We know, but thats what we saw." said Rach

"OK, so how are we going to get her back?" asked Dani

"We're going to wait until tomorrow. We'll plan then." said Leo

"WHAT!?" Yelled Raph

"We wait until tomorrow, then we'll go after her." Leo repeated.

"NO!" said Raph "Lilly doesn't have that kind of time."

"Why not?" askes Leo

"Lilly is six months pregnant." said Raph

"What!?" Shouted Leo looking at raph, in shocked. "Tell me your kidding!"

"I'm not kidding. We're having a baby." said Raph

"Then, Lets go get our sister back." said Dani and Rach together. They look at each other, then burst out laughing. Soon everyone was laughing too. Then they were ready to go and find Lilly.

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><p><strong>So, I finished my story, Secrets, And I will be writing a new story. Its called A Wolfs Past, I adopted it from Shadis1000s. I love her original story and I also Goodstoryfans version, of the story. She also adopted it and wrote it her way. she has given her blessing for me to write this story. So R&amp;R, I will be continuing with this story. I will write a sequel for Secrets.<strong>


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